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    Home » Baking Recipes » Cakes » Even Healthier Chocolate Quinoa Cupcakes

    Even Healthier Chocolate Quinoa Cupcakes

    Published: Apr 7, 2022 by Elaine · This post may contain Amazon affiliate links · As an Amazon Associate I earn from qualifying purchases. This blog generates income via ads · 13 Comments

    Jump to Recipe Print Recipe
    image with text for flourless quinoa chocolate cupcakes.
    image with text for quinoa chocolate cupcakes.

    These Gluten-free Quinoa Chocolate Cupcakes are deliciously moist with a rich dark chocolate flavour. They can be made without refined sugar! These flourless cupcakes are perfect for a birthday or special dessert when topped with whipped chocolate coconut milk frosting.

    3 quinoa chocolate quinoa cupcakes in yellow cupcake cases.

    Chocolate Quinoa Cupcakes:  let's bring back an old favourite! Do you remember when Chocolate Quinoa Cake first appeared on the scene a few years ago? We all felt like we were making a healthier choice by adding quinoa to our cake batter. And now this recipe for even healthier chocolate quinoa cupcakes satisfies all my criteria for a cupcake!

    Jump to:
    • ❤️ Why you'll love these quinoa cupcakes
    • 🛒 Ingredients and substitutions
    • 🔪 Instructions
    • How to make whipped chocolate coconut frosting
    • 🔁 Possible Variations
    • 👍🏼 Helpful Tips to make quinoa chocolate cupcakes
    • ❓Reader's Questions
    • Storage and freezing instructions
    • 🗒 More gluten-free cake recipes
    • 📖 Recipe

    ❤️ Why you'll love these quinoa cupcakes

    • they feature dark, rich chocolate
    • they're moist and tender
    • they can be made with plant-based milk
    • and they are free of gluten!

    🛒 Ingredients and substitutions

    You'll find a complete list of ingredients with amounts in the recipe card below. But before we get to the full recipe, here are a few notes about some of the key ingredients.

    • cooked quinoa: Quinoa can increase by 3 times when cooked, so you'll need to cook ⅔ cup of dry quinoa with a little less than 1 ⅓ cups of water.
    • milk: You can use any type of milk, plant-based or dairy milk.
    • butter: you can use all butter or a combination of butter and coconut oil
    • sugar: I've tested this recipe several times with both granulated sugar or coconut sugar.
    • cocoa powder: unsweetened.
    overhead view of 5 quinoa chocolate cupcakes on a plate.

    🔪 Instructions

    Here's an overview of what you'll do to make this recipe perfectly. You'll find complete instructions in the recipe card at the end of this post.

    You'll start by cooking the quinoa and letting it cool while you prepare the rest of the recipe.

    Next, you'll prepare your baking pans. This recipe will make 18 muffins or 12 regular muffins and 18 mini muffins. Alternatively, it will make two 8-inch round cakes or one 9 x 13-inch cake.

    After combining the milk, eggs and vanilla in a blender, you'll add the cooled quinoa, melted butter and coconut oil to the blender. Sift the sugar, cocoa, baking powder and baking soda, then add the blended ingredients to the dry ingredients.

    Fill the muffin tins and bake!

    Once they're completely cool, frost them with chocolate coconut milk frosting.

    wet ingredients in a blender, dry ingredients in a bowl
    1. Combine the wet ingredients in a blender and the dry ingredients in a bowl.
    pouring wet ingredients into dry ingredients in a bowl
    2. Add the wet ingredients to the dry ingredients.
    Combining wet and dry ingredients for chocolate quinoa cupcakes.
    3. Stir until well combined.
    filling mini muffin tins
    4. Fill muffin tins ¾ full.

    How to make whipped chocolate coconut frosting

    1. First, melt the chocolate chips in a glass bowl suspended over simmering water.
    2. Remove the bowl from the heat, then stir in the hardened portion of a can of coconut milk.
    3. Stir until it has melted and is well combined, and then allow it to cool completely before whipping it.
    4. Chill it in the fridge.

    Tip: If you make sure to wait until it is completely chilled and beginning to harden before you whip it, you'll be happy with the results. It holds its shape and makes decorating with a piping bag a breeze. Some brands of coconut milk will become firm faster than others.

    If you find it has hardened too much to whip, let it sit at room temperature for a few minutes until slightly softened.

    adding coconut milk to melted chocolate
    1. Add hardened coconut milk to melted chocolate.
    stirring chocolate coconut milk frosting
    2. Stir until no lumps of coconut milk remain.

    🔁 Possible Variations

    I've made this recipe many times, as cake, as muffins, and as cupcakes and it's always popular. I also like to make these as mini cupcakes for those who want a tiny taste!

    Mini chocolate quinoa cupcakes with chocolate coconut frosting and sprinkles on a white plate.
    Quinoa chocolate mini cupcakes frosted with chocolate coconut milk frosting and sprinkles.

    I adapted the original recipe that appeared in Quinoa 365. I replaced the milk with a plant-based alternative and reduced the amount of granulated sugar and replaced it with coconut sugar. Best of all, I added a fabulous whipped chocolate frosting made with coconut milk.

    👍🏼 Helpful Tips to make quinoa chocolate cupcakes

    Prepare ahead

    Make sure you have a can of full-fat coconut milk chilling in the refrigerator for 24 hours.

    Cook and cool the quinoa. Please note that the recipe requires 2 cups of COOKED quinoa, not dry. Cook ⅔ cup of dry quinoa in 1 ⅓cups of water to yield 2 cups of cooked quinoa. Measure the cooked quinoa before adding it as sometimes it yields a little more than 2 cups.

    Choose your sugar

    The original recipe from Quinoa 365 called for 1 ½ cups of granulated sugar. I find 1 ¼ cups is enough. I've used both coconut sugar and granulated sugar.

    Both types of sugar make a delicious chocolate cupcake!

    Use a blender

    If you have a high-speed blender like a Vitamix or a Blendtec, definitely use it for this recipe! It breaks down the quinoa very quickly, so there are no little lumpy seeds in the finished product. I would imagine a regular blender or food processor could do the same with just a little more processing time.

    Expect flat cupcakes

    This recipe does not produce cupcakes with a high rounded dome. They do rise and they have a light texture, but they often sink a little after baking. You can make that rounded dome look with frosting if you'd like.

    ❓Reader's Questions

    Is quinoa just a trendy food?

    With the publication of the popular cookbook Quinoa 365 way back in 2010, quinoa became a trendy food.

    Advertised as gluten-free, wheat-free and nutrient-packed, we were adding it to everything: stir-fries, salads, burrito bowls, muffins, and yes, even chocolate cake. Later, it played second fiddle to chia seeds and goji berries as they rose in the food trend charts and we experimented with these superfoods.

    But quinoa's popularity has resurged once again, and it is now higher than ever. It's an ancient crop, grown in the Andes. While it is a grain crop, it is grown for its seeds, the part that we eat. Quinoa is a good source of protein, it's gluten-free, and it is easy to digest.

    Storage and freezing instructions

    To store: Frosted cupcakes need to be refrigerated. It's best to store them in an airtight container.

    To freeze: These quinoa cupcakes freeze beautifully. Freeze in an airtight container for up to 3 months.

    Serve these flourless chocolate cupcakes and wait for chocolatey smiles all around!

    🗒 More gluten-free cake recipes

    • Paleo Carrot Cake Cupcakes with Coconut Butter Frosting
    • Gluten-free Apple Cinnamon Coffee Cake
    • Gluten-Free Spiced Applesauce Cake
    • Gluten-Free Mini Apple Bundt Cakes

    When you make these gluten-free quinoa chocolate cupcakes, please leave a comment and a star rating below. Thanks in advance! Subscribe to my newsletter and receive new recipes delivered straight to your inbox once a week.

    This recipe was originally published in 2016. It has been updated with extra information and new photos.

    📖 Recipe

    quinoa chocolate cupcakes in yellow cupcake cases.

    Gluten-free Quinoa Chocolate Cupcakes

    These Chocolate Quinoa Cupcakes are rich, uber-chocolately and gluten-free.
    Print Pin Rate
    Course: Baked Goods, Desserts
    Cuisine: American
    Diet: Gluten Free
    Prep Time: 40 minutes
    Cook Time: 27 minutes
    Total Time: 1 hour 7 minutes
    Servings: 18
    Calories: 285kcal
    Author: Elaine
    Prevent your screen from going dark

    Ingredients

    • 2 cups cooked quinoa, see note below
    • ⅓ cup milk, plant-based or dairy milk
    • 4 large eggs
    • 1 teaspoon vanilla extract
    • ½ cup melted butter
    • ¼ cup melted coconut oil
    • 1 ¼ cups sugar granulated sugar or coconut palm sugar
    • 1 cup unsweetened cocoa powder
    • ½ teaspoon baking soda
    • 1 ½ teaspoons baking powder
    • ½ teaspoon sea salt

    Whipped Chocolate Coconut Cream Frosting

    • 1 14 ounce can full-fat coconut milk, refrigerated overnight
    • 2 cups chocolate chips* use Enjoy Life brand for paleo diet

    Instructions

    • Cook ⅔ cup dry quinoa in 1 ⅓ cups of water. ( ⅔ cup of quinoa cooked in 1 ⅓ cups water will yield approximately 2 cups of cooked quinoa.) Spread out on a baking sheet to cool.
    • Heat oven to 350°F. Line 12 to 18 muffin tins with parchment paper liners or 12 muffin tins and 18 mini muffin tins. Alternatively, line two 8″ round pans or one 9 x 13″ pan with parchment paper.
    • Mix the milk, eggs and vanilla in a blender or food processor.
    • Add the cooked and cooled quinoa, butter, and coconut oil to the blender. This is where a high-speed blender like a Vitamix or a Blendtec comes in handy, as it will grind the cooked quinoa, preventing a lumpy texture in the cooked cake.
    • Sift the sugar, cocoa, baking powder, baking soda and sea salt in a large bowl.
    • Add the wet ingredients from the blender to the dry ingredients in the bowl and mix until thoroughly combined. Fill lined muffin tins ¾ full, spreading to the edges.
    • Bake at 350 degrees for 24-27 minutes or until toothpick inserted comes out clean.Remove, let cool in tins for 10 minutes, then transfer to a cooling rack. Remove the parchment paper liners. Let cool before frosting with whipped chocolate coconut cream frosting.

    Whipped Chocolate Coconut Cream Frosting

    • Melt chocolate in a bowl over, not in, simmering water.
    • Remove the can of coconut milk from the refrigerator. Carefully open it and scoop the hardened milk from the can into the chocolate, saving the liquid for another use. Stir until melted and combined. Remove from heat, let cool.
    • When completely cool and just beginning to harden slightly, beat with an electric mixer until light and fluffy.
    • Frost. Makes 18 cupcakes or 12 cupcakes and 12 - 18 mini cupcakes.

    Nutrition

    Calories: 285kcal | Carbohydrates: 33g | Protein: 5g | Fat: 17g | Saturated Fat: 12g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 55mg | Sodium: 182mg | Potassium: 286mg | Fiber: 3g | Sugar: 21g | Vitamin A: 221IU | Vitamin C: 1mg | Calcium: 98mg | Iron: 1mg
    Tried this Recipe? Pin it for Later!Mention @enessman or tag #flavourandsavour!

    More Cakes and Cupcakes

    • Gluten-Free Blueberry Lemon Coffee Cake
    • Flourless Nectarine Ricotta Cake
    • One-Bowl Flourless Lemon Almond Cake
    • Gluten-free Gingerbread Cake with Vanilla Orange Frosting

    Reader Interactions

    Comments

    1. Laura

      May 06, 2022 at 12:40 pm

      5 stars
      Love these! They are moist and chocolately -- you'd never guess they are gluten free

      Reply
      • Elaine

        May 06, 2022 at 1:47 pm

        Thanks! I just made another batch of these and froze half of them. Thanks for taking the time to comment!

        Reply
    2. Penelope

      June 28, 2020 at 12:54 pm

      Can’t wait to try your recipe! Any thoughts on using date sugar?
      Thanks

      Reply
      • Flavour & Savour

        June 28, 2020 at 1:10 pm

        I haven't tried it myself, but date sugar can usually be used as a 1:1 replacement for coconut sugar or granulated sugar. It should work just fine! It will probably give it a rich flavour, too. Let me know if you try it.

        Reply
    3. Laura

      November 19, 2017 at 8:51 am

      5 stars
      Can this be made in cake pans?

      Reply
      • Flavour & Savour

        June 28, 2020 at 1:06 pm

        Yes, it can. It may take a little longer to bake. You'll know it's done when a toothpick inserted in the center comes out clean.

        Reply
    4. Lisa Solonynko

      April 10, 2017 at 7:41 am

      I am so excited to make this. I have a quick question before I get started. Are you using Imperial, Metric or US Standard measurements. Since this is a cupcake recipe, I want to make sure I get the measurements right. Thanks so much, I can't wait to make this for Easter.

      Reply
      • Flavour & Savour

        April 10, 2017 at 10:44 am

        Hi Lisa,
        I use US Standard measurements. Note, however, that the can of coconut milk I used was 14 oz. In Canada, as you know, they are sometimes only marked in millilitres. Many cans of different brands of coconut milk are 400 ml which is not an exact conversion. However, in the frosting recipe, it really won't make any difference.

        Reply
    5. Laura

      March 13, 2016 at 12:31 pm

      5 stars
      Uber-chocolatey is right! These are delicious.

      Reply
      • Flavour & Savour

        March 13, 2016 at 12:36 pm

        Thanks Laura! Can we ever have too much chocolate?

        Reply
        • Laura

          March 14, 2016 at 12:23 pm

          5 stars
          Never!

    6. Bethany @ athletic avocado

      March 03, 2016 at 5:08 pm

      Adding quiona in place of flavor is GENIUS! Not only does it up the nutritional value, but Im sure it lends the perfect texture to these cupcakes!

      Reply
      • Flavour & Savour

        March 04, 2016 at 7:35 am

        Thanks Bethany, I was concerned that there would be little quinoa lumps in it, but no--the blender took care of that! Thanks for your comment.

        Reply

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    Elaine from Flavour and Savour

    Welcome! I'm Elaine

    I create delicious gluten-free recipes that everyone can make. I’m here to show you that gluten-free eating doesn’t have to be complicated! I’ll help you make healthy meals that you’ll want to share with family and friends. About Me!

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